pyproject.toml: add some dir; mcdock.py,unidock_pipeline.py: Path-->str

dptech-corp · Apr 9, 2024 · 767e023 · 767e023
1 parent 3311fcc
commit 767e023
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Showing 6 changed files with 6 additions and 4,119 deletions.
diff --git a/unidock_tools/pyproject.toml b/unidock_tools/pyproject.toml
@@ -30,7 +30,8 @@ classifiers = [
 ]
 
 [tool.setuptools.package-data]
-"*" = ["*.dat"]
+"*" = ["*/templates/*", "*/receptor_topology/bin/*","*/receptor_topology/data/*"]
+
 
 [project.urls]
 Homepage = "https://github.com/dptech-corp/Uni-Dock"
@@ -54,4 +55,4 @@ reportMissingImports = false
 reportMissingModuleSource = false
 reportAttributeAccessIssue = false
 reportIncompatibleMethodOverride = false
-reportCallIssue = false
+reportCallIssue = false
diff --git a/unidock_tools/src/unidock_tools/application/mcdock.py b/unidock_tools/src/unidock_tools/application/mcdock.py
@@ -87,7 +87,7 @@ def __init__(self,
         if receptor.suffix == ".pdb":
             #pdb2pdbqt(receptor, workdir.joinpath(receptor.stem + ".pdbqt"))
             #receptor = workdir.joinpath(receptor.stem + ".pdbqt")
-            receptor_pdbqt_file_name = receptor_preprocessor(receptor, working_dir_name=workdir)
+            receptor_pdbqt_file_name = receptor_preprocessor(str(receptor), working_dir_name=str(workdir))
             self.receptor = receptor_pdbqt_file_name
         if receptor.suffix != ".pdbqt":
             logging.error("receptor file must be pdb/pdbqt format")

diff --git a/unidock_tools/src/unidock_tools/application/unidock_pipeline.py b/unidock_tools/src/unidock_tools/application/unidock_pipeline.py
@@ -84,7 +84,7 @@ def __init__(self,
         if receptor.suffix == ".pdb":
             ###pdb2pdbqt(receptor, workdir.joinpath(receptor.stem + ".pdbqt"))
             ###receptor = workdir.joinpath(receptor.stem + ".pdbqt")
-            receptor_pdbqt_file_name = receptor_preprocessor(receptor, working_dir_name=workdir)
+            receptor_pdbqt_file_name = receptor_preprocessor(str(receptor), working_dir_name=str(workdir))
             self.receptor = receptor_pdbqt_file_name
         if receptor.suffix != ".pdbqt":
             logging.error("receptor file must be pdb/pdbqt format")

diff --git a/unidock_tools/src/unidock_tools/modules/docking/unidock.py b/unidock_tools/src/unidock_tools/modules/docking/unidock.py
@@ -45,7 +45,7 @@ def __init__(self,
             size_z = min(size_z*2, 25)
 
         if scoring.lower() == "ad4":
-            map_prefix = os.path.join(working_dir_name, 'protein.maps.fld')
+            map_prefix = os.path.join(self.workdir, 'receptor_grids','protein_conf_0', 'protein.maps.fld')
             cmd += ["--maps", str(map_prefix)]
         else:
             cmd += ["--receptor", str(receptor)]
@@ -92,28 +92,6 @@ def __init__(self,
 
         self.pre_result_ligands = [Path(os.path.join(output_dir, f"{l.stem}_out.sdf")) for l in ligands]
 
-    def check_env(self, use_ad4: bool = False):
-        if not shutil.which("unidock"):
-            raise ModuleNotFoundError("UniDock is not installed.")
-        if use_ad4:
-            mgltools_python_path = shutil.which("pythonsh")
-            if not mgltools_python_path:
-                raise ModuleNotFoundError("MGLTools is not installed.")
-            prepare_gpf4_script_path = os.path.join(
-                os.path.dirname(os.path.dirname(mgltools_python_path)),
-                "MGLToolsPckgs",
-                "AutoDockTools",
-                "Utilities24",
-                "prepare_gpf4.py",
-            )
-            if not os.path.exists(prepare_gpf4_script_path):
-                raise ModuleNotFoundError("MGLTools is not installed.")
-            if not shutil.which("autogrid4"):
-                raise ModuleNotFoundError("AutoGrid4 is not installed.")
-            self.mgltools_python_path = mgltools_python_path
-            self.prepare_gpf4_script_path = prepare_gpf4_script_path
-            self.ad4_map_data_path = str(Path(__file__).parent.parent.parent.joinpath("data/docking/AD4.1_bound.dat"))
-
 
     def run(self):
         resp = subprocess.run(